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Questions tagged [cox-regression]

The term Cox regression model (omitting proportional hazards) is sometimes used to describe the extension of the Cox model to include time-dependent factors. However, this usage is potentially ambiguous since the Cox proportional hazards model can itself be described as a regression model.

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How to calculate the survival function in R for a glmnet cox family?

I have a sample data of 583 type 2 diabetes patients and want to calculate the 5 year incidence probability of an event for every patient. Variables which were collected are time to an event variable censored at 5 years, event status and 38…
Faiz Yusufi
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How to modify the output of my COXPH image drawn by cph.plot_covariate_groups

I do not know how I can modify the output image provide by lifelines since I am unfamiliar with "cph.plot_covariate_groups". Unfortunately, there seems no detailed description about it in the link here;…
user9690450
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MLR: Extracting the names of the covariates with non-zero coefficients in CoxBoost

I am using mlr to create a survival model with the learner cv.CoxBoost and 5-fold cross-validation. (Yes I realise cv.CoxBosst has CV built in, but I am adding another level to be consistent with the other learners I am comparing it against). I need…
panda
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Linear Box Cox Transformation for different parameters for dependent variable/ and independent vaiable

I've been stuck on this for quite some time. Is there a command in R that will create a Box Cox Linear transformation that has a different a parameter for my independent variable and dependent variable? chicago.reg <- lm(data = Chichagodata, sprice…
AlexisRiveraAndrade
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How can I visualize an interaction in cox model in r?

I fitted a model and had a significant interaction effect. How can I plot this in a graphic? It follows a toy example (only for illustration purposes): library(survival) # includes bladder data set library(survminer) fit2 <- coxph(Surv(stop, event)…
Guilherme Parreira
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Prediction limit in normal regression and survival regression

I am trying to predict the duration it takes for gas pipes to leak. I used 15 features which the most important one is “pipe installation year”. The latest leak data that I have is for a leak that happened in 2017 and that pipe was installed in 2009…
Ehsan Estiri
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IDI.INF function to compare two Cox regression models, error?

I want to use the IDI.INF function from the survIDINRI package to compare the performance of two Cox regression models using a database of 15000 participants. I used this script: D=subset(Dataset, select=c("time","status","Var1","Var2","Var3",…
F. Laplante
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How to perform vuong test for cox regression model using R package

It is said vuong test can be used to compare two regression models that are not nested. But I wonder how to do it for cox regression models. Thanks
kuibao li
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Deviance residuals diagnostics on a Cox model with 13 independent covariates - any way I can get plots for each and every covariate?

I am new to survival statistics and to these forums, so forgive me for not knowing the lingo or the proper way of inquiry. WIll give it my best shot. I am aiming to perform some cox regressions and want to do some basic diagnostics on its goodness…
Hakim
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C-statistics and 95% confidence interval for Cox-model with time-dependent covariates

I am performing Cox regression with a time-dependent covariate. I´m specifically interested in calculating the 95% confidence interval of the Concordance index. The standard summary of the coxph model however only returns the Concordance index and…
user86533
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Linear predictor from coefficients of Cox PH model

I need to calculate the linear predictor of a Cox PH model by hand. I can get continuous and binary variables to match the output of predict.coxph (specifying 'lp') but I can't seem to figure out how to calculate it for categorical variables with…
Michelle
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Cox model concordance value is different from c-index caculated by mlr

If I train a cox model using resampling with 5-fold cross validation in mlr, the value for Concordance that is output by printing the summary of the Cox model for each fold is different from the value for cindex that is calculated by mlr. Am I…
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MLR - Resampling of cox model

If I train a single Cox PH model in mlr, I can print a summary that shows the statistical significance of each predictor as shown below. But if I use resampling eg 5-fold cross validation, is there any way to get this information, perhaps aggregated…
panda
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R - Different length in variable and residuals from the model

I'm trying to find the the best variable transformation that yields linearity in log hazard or log cumulative hazard of a Cox proportional Hazard model. As those ar research data, I cannot publish them here. For this I'm trying to plot the variable…
ecjb
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Plot the effect of time dependent variable on survival curve from coxph model in R?

I have fitted a coxph model with time dependent variable of weight and time independent variables as following: id start stop death weight age smoke 1 0 1 0 60 60 0 2 0 1 0 55 57 1 2 1 2 1 60 …
Joey Zhou
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